Automated alignment for each protein was performed using ClustalX [ 58], after which, alignment was manually adjusted with MacClade 4.06 [ 59].
Also, as shown below, the length of 454 reads proves useful for detecting SNVs and small InDels in highly variable regions, for which the alignment with Illumina reads is not feasible.
The sequences of the NBS domains were used to build a phylogeny tree of the annotated R-genes with the "One click" option of the Phylogeny.fr web service, which includes alignment with MUSCLE, curating using Gblocks, phylogeny analysis with PhyML, and tree rendering using TreeDyn [ 40].
The Solexa reads were mapped at increasing coverage onto the 25× GSFLX assembly using SOAP software[ 18], which allows alignments with gaps.
However, these studies do show markedly reduced tracheobronchial clearance in patients with known PCD compared with healthy individuals which is in alignment with our results.
High temperature showed an inconsistent effect on stem lodging resistance, which was in alignment with the engineering mechanics theory and supported by the anatomical observations.
In general, a characteristic local maximum can be expected if the D/P ratio is in the range of 0.7 to 0.8, which is in alignment with estimates published elsewhere [27 29].
In this paper, we simulated both hop count as well as link metric for 1500 bytes (with respect to our network model which is in alignment with MTM [23]) in comparison to our proposed metric (e.g., packet function/size) over Dijkstra as well as extended version of Dijkstra algorithm.
The open-book examination measures the application of knowledge, which is in alignment with PBL.
First, the C. savignyi genome has ambiguous and incomplete regions, which prevented sufficient alignment with the C. intestinalis genome.
